Do all paths lead to Rome? How reliable is umbrella sampling along a single path?
Molecular dynamics (MD) simulations are widely applied to estimate absolute binding free
energies of protein–ligand and protein–protein complexes. A routinely used method for …
energies of protein–ligand and protein–protein complexes. A routinely used method for …
Automated adaptive absolute binding free energy calculations
Alchemical absolute binding free energy (ABFE) calculations have substantial potential in
drug discovery, but are often prohibitively computationally expensive. To unlock their …
drug discovery, but are often prohibitively computationally expensive. To unlock their …
Optimal Molecular Design: Generative Active Learning Combining REINVENT with Precise Binding Free Energy Ranking Simulations
Active learning (AL) is a specific instance of sequential experimental design and uses
machine learning to intelligently choose the next data point or batch of molecular structures …
machine learning to intelligently choose the next data point or batch of molecular structures …
Equilibrium and Nonequilibrium Ensemble Methods for Accurate, Precise and Reproducible Absolute Binding Free Energy Calculations
Free energy calculations for protein–ligand complexes have become widespread in recent
years owing to several conceptual, methodological and technological advances. Central …
years owing to several conceptual, methodological and technological advances. Central …
Accuracy and Reproducibility of Lipari-Szabo Order Parameters From Molecular Dynamics
TT Lai, CL Brooks III - The Journal of Physical Chemistry B, 2024 - ACS Publications
The Lipari-Szabo generalized order parameter probes the picosecond to nanosecond time
scale motions of a protein and is useful for rationalizing a multitude of biological processes …
scale motions of a protein and is useful for rationalizing a multitude of biological processes …
Uncertainty Visualization Challenges in Decision Systems with Ensemble Data & Surrogate Models
S Molnar, JD Laurence-Chasen, Y Duan… - … IEEE Workshop on …, 2024 - ieeexplore.ieee.org
Uncertainty visualization is a key component in translating important insights from ensemble
simulation data into actionable decision-making by visually conveying various aspects of …
simulation data into actionable decision-making by visually conveying various aspects of …
Optimal Molecular Design: Generative Active Learning Combining REINVENT with Absolute Binding Free Energy Simulations
Active learning (AL) is a specific instance of sequential experimental design and uses
machine learning to intelligently choose the next data point or batch of molecular structures …
machine learning to intelligently choose the next data point or batch of molecular structures …
Do all roads lead to Rome? Convergence issues in umbrella sampling simulations
N Aho, G Groenhof, P Buslaev - 2023 - chemrxiv.org
Molecular dynamics (MD) simulations are widely applied to estimate absolute binding free
energies of protein-ligand and protein-protein complexes. A routinely used method for …
energies of protein-ligand and protein-protein complexes. A routinely used method for …